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[R-pkg-devel] "invalid 'envir' argument" note from R-devel

Mon, Jul 13, 2015 4:01 PM

It happened in r68597.  In my example, I hadn't imported the data()
function from utils; when I did that, it was fixed.

Not sure why the error is complaining about the envir argument.

Duncan Murdoch

On 13/07/2015 6:47 PM, John Fox wrote:

Dear Duncan and Peter,

I've just arrived at more or less the same thing:

	foo <- function() data(package="MASS")

	bar <- function() data(package="MASS", envir=.GlobalEnv)

	baz <- function() data(package="MASS", envir=globalenv())

all trigger the note when included with the Rcmdr sources:

	* checking R code for possible problems ... NOTE
	bar: Error while checking: invalid 'envir' argument
	baz: Error while checking: invalid 'envir' argument
	foo: Error while checking: invalid 'envir' argument 

The envir argument to data() defaults to .GlobaEnv .

I hope this helps,
 John

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com]
Sent: July-13-15 6:32 PM
To: John Fox; 'peter dalgaard'
Cc: r-package-devel at r-project.org
Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-devel

On 13/07/2015 5:23 PM, John Fox wrote:

Dear Peter,

-----Original Message-----
From: peter dalgaard [mailto:pdalgd at gmail.com]
Sent: July-13-15 4:52 PM
To: John Fox
Cc: r-package-devel at r-project.org
Subject: Re: [R-pkg-devel] "invalid 'envir' argument" note from R-

devel

Yes, there was a similar note from Alexandra Kuznetsova a couple of

days

Sorry, I didn't notice that.

ago. Look unintentional, but it is not easy to spot what triggers it.

If

someone could cook up a minimal example, or - maybe easier given the
relatively short timeframe - bisect their way to the exact svn

revision

that triggered it, it might help in getting it fixed.

I'm afraid that I'm not set up to build R-devel and I'm about to leave

town

for three weeks. I'll see if I can produce a simpler example

triggering the

error, however.

Hana Sevcikova posted a simple example.  I'll bisect on it.

Here's her example:

e <- new.env()
data("mydataset", envir=e)

I've substituted USArrests for "mydataset".

Duncan Murdoch

Thanks for this,
 John

-pd

On 13 Jul 2015, at 22:31 , John Fox <jfox at mcmaster.ca> wrote:

Dear list members,

I'm getting a new note from R-devel that I haven't seen before when

checking

the development version of the Rcmdr package:

	* checking R code for possible problems ... NOTE
	readDataFromPackage: Error while checking: invalid 'envir' argument

This note doesn't appear in R 3.2.1.

My session info:

-------- snip ----------

R Under development (unstable) (2015-07-12 r68650)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_Canada.1252  LC_CTYPE=English_Canada.1252
LC_MONETARY=English_Canada.1252
[4] LC_NUMERIC=C                    LC_TIME=English_Canada.1252

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] tools_3.3.0

-------- snip ----------

I can't even localize the problem in readDataFromPackage(). There

are

only

two places in this function where there's a function call with an

envir

argument, and I still get the note if I comment these out. As well,
readDataFromPackage() seems to work as intended -- there is no

obvious

error

in it.

FWIW, here's readDataFromPackage(). The complete sources for the

development

version of the Rcmdr package are on R-Forge.

-------- snip ----------

readDataFromPackage <- function() {
	env <- environment()
	datasets <- NULL
	initializeDialog(title=gettextRcmdr("Read Data From Package"))
	dsname <- tclVar("")
	package <- NULL
	enterFrame <- tkframe(top)
	entryDsname <- ttkentry(enterFrame, width="20",

textvariable=dsname)

	packages <- sort(.packages())
	packages <- packages[! packages %in% c("base", "stats")]
	packages <- packages[sapply(packages, function(package){
						ds <-
data(package=package)$results
						if (nrow(ds) == 0)
return(FALSE)
						ds <- ds[, "Item"]
						valid <- sapply(ds,
is.valid.name)
						length(ds[valid]) > 0
					})]
	packageDatasetFrame <- tkframe(top)
	packageFrame <- tkframe(packageDatasetFrame)
	max.height <- getRcmdr("variable.list.height")
	packageBox <- tklistbox(packageFrame, height=min(max.height,
length(packages)),
           exportselection="FALSE",
			selectmode="single", background="white")
	packageScroll <- ttkscrollbar(packageFrame,
			command=function(...) tkyview(packageBox, ...))
	tkconfigure(packageBox, yscrollcommand=function(...)
tkset(packageScroll, ...))
	for (p in packages) tkinsert(packageBox, "end", p)
	datasetFrame <- tkframe(packageDatasetFrame)
	datasetBox <- tklistbox(datasetFrame, height=max.height,
exportselection="FALSE",
			selectmode="single", background="white")
	datasetScroll <- ttkscrollbar(datasetFrame,
			command=function(...) tkyview(datasetBox, ...))
	tkconfigure(datasetBox, yscrollcommand=function(...)
tkset(datasetScroll, ...))
	onPackageSelect <- function(){
		assign("package",
packages[as.numeric(tkcurselection(packageBox)) + 1], envir=env)
		datasets <<- data(package=package)$results[,3]
		valid <- sapply(datasets, is.valid.name)
		datasets <<- datasets[valid]
		tkdelete(datasetBox, "0", "end")
		for (dataset in datasets) tkinsert(datasetBox, "end",
dataset)
		tkconfigure(datasetBox, height=min(max.height,
length(datasets)))
		firstChar <- tolower(substr(datasets, 1, 1))
		len <- length(datasets)
		onLetter <- function(letter){
			letter <- tolower(letter)
			current <- 1 +
round(as.numeric(unlist(strsplit(tclvalue(tkyview(datasetBox) ), "
"))[1])*len)
			mat <- match(letter, firstChar[-(1:current)])
			if (is.na(mat)) return()
			tkyview.scroll(datasetBox, mat, "units")
		}
		onA <- function() onLetter("a")
		onB <- function() onLetter("b")
		onC <- function() onLetter("c")
		onD <- function() onLetter("d")
		onE <- function() onLetter("e")
		onF <- function() onLetter("f")
		onG <- function() onLetter("g")
		onH <- function() onLetter("h")
		onI <- function() onLetter("i")
		onJ <- function() onLetter("j")
		onK <- function() onLetter("k")
		onL <- function() onLetter("l")
		onM <- function() onLetter("m")
		onN <- function() onLetter("n")
		onO <- function() onLetter("o")
		onP <- function() onLetter("p")
		onQ <- function() onLetter("q")
		onR <- function() onLetter("r")
		onS <- function() onLetter("s")
		onT <- function() onLetter("t")
		onU <- function() onLetter("u")
		onV <- function() onLetter("v")
		onW <- function() onLetter("w")
		onX <- function() onLetter("x")
		onY <- function() onLetter("y")
		onZ <- function() onLetter("z")
		for (letter in c(letters, LETTERS)){
			tkbind(datasetBox, paste("<", letter, ">", sep=""),
					get(paste("on", toupper(letter),
sep="")))
		}
		onClick <- function() tkfocus(datasetBox)
		tkbind(datasetBox, "<ButtonPress-1>", onClick)
	}
	onDatasetSelect <- function(){
		tclvalue(dsname) <-
datasets[as.numeric(tkcurselection(datasetBox)) + 1]
	}
	firstChar <- tolower(substr(packages, 1, 1))
	len <- length(packages)
	onLetter <- function(letter){
		letter <- tolower(letter)
		current <- 1 +
round(as.numeric(unlist(strsplit(tclvalue(tkyview(packageBox) ), "
"))[1])*len)
		mat <- match(letter, firstChar[-(1:current)])
		if (is.na(mat)) return()
		tkyview.scroll(packageBox, mat, "units")
	}
	onA <- function() onLetter("a")
	onB <- function() onLetter("b")
	onC <- function() onLetter("c")
	onD <- function() onLetter("d")
	onE <- function() onLetter("e")
	onF <- function() onLetter("f")
	onG <- function() onLetter("g")
	onH <- function() onLetter("h")
	onI <- function() onLetter("i")
	onJ <- function() onLetter("j")
	onK <- function() onLetter("k")
	onL <- function() onLetter("l")
	onM <- function() onLetter("m")
	onN <- function() onLetter("n")
	onO <- function() onLetter("o")
	onP <- function() onLetter("p")
	onQ <- function() onLetter("q")
	onR <- function() onLetter("r")
	onS <- function() onLetter("s")
	onT <- function() onLetter("t")
	onU <- function() onLetter("u")
	onV <- function() onLetter("v")
	onW <- function() onLetter("w")
	onX <- function() onLetter("x")
	onY <- function() onLetter("y")
	onZ <- function() onLetter("z")
	for (letter in c(letters, LETTERS)){
		tkbind(packageBox, paste("<", letter, ">", sep=""),
				get(paste("on", toupper(letter), sep="")))
	}
	onClick <- function() tkfocus(packageBox)
	tkbind(packageBox, "<ButtonPress-1>", onClick)
	onOK <- function(){
		datasetName <-
datasets[as.numeric(tkcurselection(datasetBox)) + 1]
		dsnameValue <- tclvalue(dsname)
		if (dsnameValue != "" && is.null(package)){
			closeDialog()
			if (is.element(dsnameValue, listDataSets())) {
				if ("no" ==
tclvalue(checkReplace(dsnameValue, gettextRcmdr("Data set")))){
					if (GrabFocus()) tkgrab.release(top)
					tkdestroy(top)
					readDataFromPackage()
					return()
				}
			}
			save.options <- options(warn=2)
			check <- try(eval(parse(text=logger(paste("data(",
dsnameValue, ")", sep=""))),
							envir=.GlobalEnv),
silent=TRUE)
			options(save.options)
			if (class(check) == "try-error"){
				errorCondition(recall=readDataFromPackage,

message=sprintf(gettextRcmdr("Data set %s does not exit"),

dsnameValue))

				return()
			}
			activeDataSet(dsnameValue)
			tkfocus(CommanderWindow())
		}
		else{
			if (is.null(package)) {
				errorCondition(recall=readDataFromPackage,
message=gettextRcmdr("You must select a package."))
				return()
			}
			if (length(datasetName) == 0) {
				errorCondition(recall=readDataFromPackage,
message=gettextRcmdr("You must select a data set.")    )
				return()
			}
			if (is.element(datasetName, listDataSets())) {
				if ("no" ==
tclvalue(checkReplace(datasetName, gettextRcmdr("Data set")))){
					if (GrabFocus()) tkgrab.release(top)
					tkdestroy(top)
					readDataFromPackage()
					return()
				}
			}
			closeDialog()
			command <- paste("data(", datasetName, ',
package="', package, '")', sep="")
			result <- justDoIt(command)
			logger(command)
			if (class(result)[1] !=  "try-error")
activeDataSet(datasetName)
			tkfocus(CommanderWindow())
		}
	}
	onDataHelp <- function(){
   datasetName <- datasets[as.numeric(tkcurselection(datasetBox)) +

1]

		dsnameValue <- tclvalue(dsname)
		if (dsnameValue == "") dsnameValue <- datasetName
		if (length(dsnameValue) == 0) Message(gettextRcmdr("No data
set selected."), type="warning")
		else if (is.null(package)) doItAndPrint(paste('help("',
dsnameValue, '")', sep=""))
		else doItAndPrint(paste('help("', dsnameValue, '",
package="', package, '")', sep=""))
	}
	OKCancelHelp(helpSubject="data")
	dataHelpButton <- buttonRcmdr(top, text=gettextRcmdr("Help on
selected data set"), command=onDataHelp)
	tkgrid(labelRcmdr(packageDatasetFrame, text=gettextRcmdr("Package
(Double-click to select)"), fg=getRcmdr("title.color"),
font="RcmdrTitleFont"),
			labelRcmdr(packageDatasetFrame, text="   "),
labelRcmdr(packageDatasetFrame, text=gettextRcmdr("Data set (Double-

click to

select)"),
					fg=getRcmdr("title.color"),
font="RcmdrTitleFont"), sticky="w")
	tkgrid(packageBox, packageScroll, sticky="nw")
	tkgrid(datasetBox, datasetScroll, sticky="nw")
	tkgrid(packageFrame, labelRcmdr(packageDatasetFrame, text="   "),
datasetFrame, sticky="nw")
	tkgrid(packageDatasetFrame, sticky="w")
	tkgrid(labelRcmdr(top, text=gettextRcmdr("OR"), fg="red"),
sticky="w")
	tkgrid(labelRcmdr(enterFrame, text=gettextRcmdr("Enter name of data
set:  "), fg=getRcmdr("title.color"), font="RcmdrTitleFont"),

entryDsname,

sticky="w")
	tkgrid(enterFrame, sticky="w")
	tkgrid(dataHelpButton, sticky="w")
	tkgrid(buttonsFrame, sticky="ew")
	tkgrid.configure(packageScroll, sticky="ns")
	tkgrid.configure(datasetScroll, sticky="ns")
	tkbind(packageBox, "<Double-ButtonPress-1>", onPackageSelect)
	tkbind(datasetBox, "<Double-ButtonPress-1>", onDatasetSelect)
	dialogSuffix(focus=entryDsname)
}

-------- snip ----------

Any insight into the problem would be appreciated.

Thanks,
John

-----------------------------------------------
John Fox, Professor
McMaster University
Hamilton, Ontario, Canada
http://socserv.socsci.mcmaster.ca/jfox/




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Thread (16 messages)

John Fox "invalid 'envir' argument" note from R-devel Jul 13 Peter Dalgaard "invalid 'envir' argument" note from R-devel Jul 13 John Fox "invalid 'envir' argument" note from R-devel Jul 13 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 13 John Fox "invalid 'envir' argument" note from R-devel Jul 13 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 13 John Fox "invalid 'envir' argument" note from R-devel Jul 13 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 13 John Fox "invalid 'envir' argument" note from R-devel Jul 13 John Fox "invalid 'envir' argument" note from R-devel Jul 13 Peter Dalgaard "invalid 'envir' argument" note from R-devel Jul 14 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 14 John Fox "invalid 'envir' argument" note from R-devel Jul 14 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 14 Dirk Eddelbuettel "invalid 'envir' argument" note from R-devel Jul 15 Duncan Murdoch "invalid 'envir' argument" note from R-devel Jul 15